Structuring referenced files

I have been using managed files up to now. Time to switch over to references masters. The concept of switching over seems easy enough. I picked up a 1 TB portable small external drive.
I realize I go to File>Relocate Masters as the basic comand to move the master files. Here's my question(s)
How do I set up the file structure on the external drive? Do I need to manually create folders to match the names of the projects in the managed library or will it automatically create such similar/parallel structure for me?
Or does it just pop them all under a generic "masters" folder?
Here's what I've done so far and it isn't looking right to me somehow. I choose a project. I went to the new external drive and created a master folder titled something like Aperture3Fall2011. I then created the projects name under that root folder. When I relocated the masters, it moved them to a "masters" folder under appropriately matching project name. Seems ok so far, rather simple.
Next project. Selected it, choose all pictures, Files>relocate masters. I created matching folders under the Aperture3Fall2011 root folder. It then proceeded to put them in the exact same previous folder as the first batch I processed. In other words, it is as if it is going to just create one huge masters file and put all masters under that one "masters" folder.
What is the structure that Aperture 3 will create automatically on the reference external disk? Or does it not automatically create the heirarchy and I have to manually create and force masters folders for each project under appropriate names?
So I guess I'm asking how to handle the external drive aspect of the whole relocate masters to referenced images deal. Do I create folders/heirarchy manually and individually per project or does it just dump them all into one masters file?
Thanks

thank you all for your help. I was able to take the referenced library that had put all master files under one "masters" folder and get them back into a managed library for Ap3.
I did what was mentioned: had to do one project at a time.
Then once I got that done, the laptop hard drive was bloated again.
Then I took my time to start yet again to reference the masters so as to free up major space on the hard drive.
The one thing I must have missed as I read about making a managed library into a referenced is that I needed to go into the "edit" option and, so to speak, build the structure using an apple template/format. Basically, that allowed me to then reference the masters on the external drive with the same basic heirarchy as what I see under my inspector tab.
Once I did that and got the hang of it, things went smoothly. I have the 1TB external FW800 now filled with masters.
I am busy now taking the external FW800 drive and copying it over to my Drobo FS in order to have a duplicate backup.
I would be interested in hearing thoughts on how you take referenced masters and how you back them up for redundancy's sake.
Thanks everyone

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    App External ID: 11130653
    Code Type:       X86-64 (Native)
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    User ID:         501
    Date/Time:       2012-10-25 08:47:06.464 +1300
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    Report Version:  10
    Interval Since Last Report:          122141 sec
    Crashes Since Last Report:           9
    Per-App Interval Since Last Report:  102826 sec
    Per-App Crashes Since Last Report:   8
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    14  com.apple.AppKit                        0x00007fff9178aed2 -[NSApplication nextEventMatchingMask:untilDate:inMode:dequeue:] + 128
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    16  com.apple.AppKit                        0x00007fff919d5709 -[NSApplication _realDoModalLoop:peek:] + 485
    17  com.apple.AppKit                        0x00007fff919d59ce -[NSApplication runModalForWindow:] + 120
    18  com.apple.Aperture                      0x0000000106f7fcb3 0x106e03000 + 1559731
    19  com.apple.Aperture                      0x0000000106e4b0b5 0x106e03000 + 295093
    20  com.apple.AppKit                        0x00007fff9187ba59 -[NSApplication sendAction:to:from:] + 342
    21  com.apple.prokit                        0x000000010831f10c -[NSProApplication sendAction:to:from:] + 101
    22  com.apple.Aperture                      0x00000001072780bf 0x106e03000 + 4673727
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    25  com.apple.AppKit                        0x00007fff9169e46f -[NSMenu _internalPerformActionForItemAtIndex:] + 36
    26  com.apple.AppKit                        0x00007fff9169e2f7 -[NSCarbonMenuImpl _carbonCommandProcessEvent:handlerCallRef:] + 135
    27  com.apple.AppKit                        0x00007fff919aa245 NSSLMMenuEventHandler + 342
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    Identifier:      com.apple.Aperture
    Version:         3.4.1 (3.4.1)
    Build Info:      Aperture-301039000000000~2
    App Item ID:     408981426
    App External ID: 11130653
    Code Type:       X86-64 (Native)
    Parent Process:  launchd [177]
    User ID:         501
    Date/Time:       2012-10-25 08:47:06.464 +1300
    OS Version:      Mac OS X 10.8.2 (12C60)
    Report Version:  10
    Interval Since Last Report:          122141 sec
    Crashes Since Last Report:           9
    Per-App Interval Since Last Report:  102826 sec
    Per-App Crashes Since Last Report:   8
    Anonymous UUID:                      C8AB497A-18DB-3A43-8663-4B28960DFA6E
    Crashed Thread:  0  Dispatch queue: com.apple.main-thread
    Exception Type:  EXC_BAD_ACCESS (SIGSEGV)
    Exception Codes: EXC_I386_GPFLT
    Application Specific Information:
    objc_msgSend() selector name: dealloc
    Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
    0   libobjc.A.dylib                         0x00007fff897cf250 objc_msgSend + 16
    1   com.apple.Aperture                      0x0000000106f2ce46 0x106e03000 + 1220166
    2   com.apple.Aperture                      0x0000000106f2cf32 0x106e03000 + 1220402
    3   com.apple.AppKit                        0x00007fff91a15ce6 -[_NSBrowserMatrixColumnViewController reloadData] + 587
    4   com.apple.AppKit                        0x00007fff91a02e23 -[NSBrowser _matrixBasedReloadColumn:] + 199
    5   libdispatch.dylib                       0x00007fff8b431f01 _dispatch_call_block_and_release + 15
    6   libdispatch.dylib                       0x00007fff8b42e0b6 _dispatch_client_callout + 8
    7   libdispatch.dylib                       0x00007fff8b4330c8 _dispatch_main_queue_callback_4CF + 275
    8   com.apple.CoreFoundation                0x00007fff899b30fe __CFRunLoopRun + 1614
    9   com.apple.CoreFoundation                0x00007fff899b26b2 CFRunLoopRunSpecific + 290
    10  com.apple.HIToolbox                     0x00007fff8df760a4 RunCurrentEventLoopInMode + 209
    11  com.apple.HIToolbox                     0x00007fff8df75e42 ReceiveNextEventCommon + 356
    12  com.apple.HIToolbox                     0x00007fff8df75cd3 BlockUntilNextEventMatchingListInMode + 62
    13  com.apple.AppKit                        0x00007fff9178b613 _DPSNextEvent + 685
    14  com.apple.AppKit                        0x00007fff9178aed2 -[NSApplication nextEventMatchingMask:untilDate:inMode:dequeue:] + 128
    15  com.apple.Aperture                      0x000000010727700d 0x106e03000 + 4669453
    16  com.apple.AppKit                        0x00007fff919d5709 -[NSApplication _realDoModalLoop:peek:] + 485
    17  com.apple.AppKit                        0x00007fff919d59ce -[NSApplication runModalForWindow:] + 120
    18  com.apple.Aperture                      0x0000000106f7fcb3 0x106e03000 + 1559731
    19  com.apple.Aperture                      0x0000000106e4b0b5 0x106e03000 + 295093
    20  com.apple.AppKit                        0x00007fff9187ba59 -[NSApplication sendAction:to:from:] + 342
    21  com.apple.prokit                        0x000000010831f10c -[NSProApplication sendAction:to:from:] + 101
    22  com.apple.Aperture                      0x00000001072780bf 0x106e03000 + 4673727
    23  com.apple.AppKit                        0x00007fff919b144c -[NSMenuItem _corePerformAction] + 406
    24  com.apple.AppKit                        0x00007fff919b113a -[NSCarbonMenuImpl performActionWithHighlightingForItemAtIndex:] + 133
    25  com.apple.AppKit                        0x00007fff9169e46f -[NSMenu _internalPerformActionForItemAtIndex:] + 36
    26  com.apple.AppKit                        0x00007fff9169e2f7 -[NSCarbonMenuImpl _carbonCommandProcessEvent:handlerCallRef:] + 135
    27  com.apple.AppKit                        0x00007fff919aa245 NSSLMMenuEventHandler + 342
    28  com.apple.HIToolbox                     0x00007fff8df4ef0a DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*, HandlerCallRec*) + 1206

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